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Version 9: fasta problems

Marlon Cole cczcole at unix.ccc.nottingham.ac.uk
Tue Jan 28 12:07:30 EST 1997

Apologies first: I'm very much a newbie to GCG admin - I'm no molecular
biologist by any means - I just happen to manage the Unix system that our
molecular biologists here use GCG on (in fact I'm not even sure that this
newsgroup is the one to post admin. problems to, so if not, do excuse my
ignorance).  Anyway, onto the problem:

I've just upgraded to Version 9 from 8.1 (on Digital Unix v.3.2D) and have
had reports from one of my users that his usual run of "fasta" searching
SwissProt:* now no longer works:
Using "fasta" and supplying a query sequence file, after the prompt:

" Search for query in what sequence(s) (* SwissProt:* *) ?"

we now get the error:

 *** Search set "SwissProt:*" could not be read! ***

I've not thrown away Version 8.1 yet, so am still able to verify that I can
run the very same query with the old version successfully.

I'm running with the version of SwissProt (release 33.0) as installed with
8.1, and note that the Version 9 CD containing SwissProt is also stamped
release 33.0, yet the versions part of the startup banner (that is the
contents of the file $GCG..ROOT/gcgcore/scriptdoc/versions.txt) is reporting
that release 34.0 is available.  I don't know if that's significant or not.

Any help or requests for further information gratefully received!

Marlon Cole                         email: Marlon.Cole at nottingham.ac.uk
Systems Section                     Tel:   0115 951 3398
Cripps Computing Centre             URL: http://www.nottingham.ac.uk/~cczcole
University of Nottingham, ENGLAND.

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